Improve NVTX Range Naming #3484
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Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Behrooz <[email protected]>
wyli
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Dec 14, 2021
Signed-off-by: Behrooz <[email protected]>
wyli
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Dec 14, 2021
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Jan 4, 2022
* Update to not include number for the name of the first range Signed-off-by: Behrooz <[email protected]> * Update CuCIM and TorchVision wrappers to include name Signed-off-by: Behrooz <[email protected]> * Update nvtx range to append undelying class for wrapper tranforms Signed-off-by: Behrooz <[email protected]> * Add new test cases to cover changes Signed-off-by: Behrooz <[email protected]> * Update cucim and torchvision check Signed-off-by: Behrooz <[email protected]>
wyli
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that referenced
this pull request
Jan 4, 2022
* Update to not include number for the name of the first range Signed-off-by: Behrooz <[email protected]> * Update CuCIM and TorchVision wrappers to include name Signed-off-by: Behrooz <[email protected]> * Update nvtx range to append undelying class for wrapper tranforms Signed-off-by: Behrooz <[email protected]> * Add new test cases to cover changes Signed-off-by: Behrooz <[email protected]> * Update cucim and torchvision check Signed-off-by: Behrooz <[email protected]>
Can-Zhao
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Jan 5, 2022
* 3415 Update WSIReader (#3417) * Update WSIReader level/location/size calculation Signed-off-by: Behrooz <[email protected]> * Update location downsampling Signed-off-by: Behrooz <[email protected]> * Update tests and add a new test case Signed-off-by: Behrooz <[email protected]> * Update few names and logics Signed-off-by: Behrooz <[email protected]> * Fix the dependency issue Signed-off-by: Behrooz <[email protected]> * Check for imagecodecs + tifffile Signed-off-by: Behrooz <[email protected]> * Remove new test case that uses too much memory Signed-off-by: Behrooz <[email protected]> * Add new case and ignore level=0 for TiffFile Signed-off-by: Behrooz <[email protected]> * Address comments Signed-off-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]> * update create_file_basename (#3436) Signed-off-by: Wenqi Li <[email protected]> * Update TiffFile backend in WSIReader (#3438) * Update TiffFile backend to read only the entire image Signed-off-by: Behrooz <[email protected]> * 3429 Enhance the scalar write logic of TensorBoardStatsHandler (#3431) * [DLMED] extract write logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * 3430 support dataframes and streams in CSVDataset (#3440) * [DLMED] add dataframe Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance CSV iterable dataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typehints Signed-off-by: Nic Ma <[email protected]> * [DLMED] add comment Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix file close issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]> * Add base class for workflows (#3445) * [DLMED] add BaseWorkflow Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] add *args, **kwargs Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> * Enhance deprecated arg for kwargs in CSV datasets (#3446) * [DLMED] fix deprecated arg Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]> * 3293 Remove extra deep supervision modules of DynUNet (#3427) * enhance dynunet Signed-off-by: Yiheng Wang <[email protected]> * fix black issue Signed-off-by: Yiheng Wang <[email protected]> * use strict=False Signed-off-by: Yiheng Wang <[email protected]> * fix black 21.12 error Signed-off-by: Yiheng Wang <[email protected]> * enhance code and update docstring Signed-off-by: Yiheng Wang <[email protected]> * 471- fixes deprecated args (#3447) * fixes deprecated args Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * improve error message if reader nott available (#3457) improve error message if reader nott available * adds the missing imports (#3462) Signed-off-by: Wenqi Li <[email protected]> * revise MILModel docstring (#3459) Signed-off-by: Wenqi Li <[email protected]> * deprecate reduction (#3464) Signed-off-by: Wenqi Li <[email protected]> * 3444 Add DatasetFunc (#3456) * [DLMED] add dataset generator Signed-off-by: Nic Ma <[email protected]> * [DLMED] add DatasetGenerator Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix wrong test Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove return Signed-off-by: Nic Ma <[email protected]> * [DLMED] update rtol for CI Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> * Add missing components to API doc (#3468) * [DLMED] add missing docs Signed-off-by: Nic Ma <[email protected]> * [DLMED] add missing components Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test Signed-off-by: Nic Ma <[email protected]> * 3466 3467 Add `channel_wise` and correct doc-string (#3469) * [DLMED] add channel-wise Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip test if before 1.7 Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]> * [DLMED] remove cls (#3475) Signed-off-by: Nic Ma <[email protected]> * Add Iteration base class (#3472) * [DLMED] add Iteration base class Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * fix link error (#3488) Signed-off-by: Yiheng Wang <[email protected]> * 3465 Support string as dtype (#3478) * [DLMED] support string dtype Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance dtype in ToCupy Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to 0.4.7 (#3483) Signed-off-by: Nic Ma <[email protected]> * Improve NVTX Range Naming (#3484) * Update to not include number for the name of the first range Signed-off-by: Behrooz <[email protected]> * Update CuCIM and TorchVision wrappers to include name Signed-off-by: Behrooz <[email protected]> * Update nvtx range to append undelying class for wrapper tranforms Signed-off-by: Behrooz <[email protected]> * Add new test cases to cover changes Signed-off-by: Behrooz <[email protected]> * Update cucim and torchvision check Signed-off-by: Behrooz <[email protected]> * 3471 3491 Add example images for intensity transforms (#3494) * [DLMED] add missing images Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix 3471 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix AsDiscrete Signed-off-by: Nic Ma <[email protected]> * Make bending energy loss invariant to resolution (#3493) * make bending energy loss invariant to resolution fixes #3485 Signed-off-by: Ebrahim Ebrahim <[email protected]> * set BendingEnergyLoss default normalize to False Maybe it's more important that the default behavior match usage of the term "bending energy" elsewhere, rather than that it be the most convenient behavior. Signed-off-by: Ebrahim Ebrahim <[email protected]> * Removes redundant casting -- ensure tuple (#3495) Signed-off-by: Wenqi Li <[email protected]> * 3498 Correct `kwargs` arg for `convert_to_torchscript` (#3499) * [DLMED] correct kwargs Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix grammar Signed-off-by: Nic Ma <[email protected]> * update tests with 1.10.1 (#3500) Signed-off-by: Wenqi Li <[email protected]> * 3501 Add dict version SavitzkyGolaySmoothd (#3502) * [DLMED] add SavitzkyGolaySmoothd Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * remove file (#3507) Signed-off-by: Wenqi Li <[email protected]> * avoid 60.0.0 (#3514) Signed-off-by: Wenqi Li <[email protected]> * [DLMED] add 6 new transform images (#3512) Signed-off-by: Nic Ma <[email protected]> * support of reversed indexing (#3508) Signed-off-by: Wenqi Li <[email protected]> * Adding Torchscript utility functions (#3138) * Adding Torchscript utility functions Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Adding Torchscript utility functions Signed-off-by: Eric Kerfoot <[email protected]> * Added test for extra files Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Nic Ma <[email protected]> * 3517 Refine AddCoordinateChannels transform (#3524) * [DLMED] change to utility transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance args Signed-off-by: Nic Ma <[email protected]> * 3521 Copyright header update (#3522) * adds missing item Signed-off-by: Wenqi Li <[email protected]> * update the contributing guide Signed-off-by: Wenqi Li <[email protected]> * update copyright headers Signed-off-by: Wenqi Li <[email protected]> * 3521 - adds a util to check the licence info (#3523) * util to check the licence info Signed-off-by: Wenqi Li <[email protected]> * update flags Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * 3350 Remove PyTorch 1.5.x related logic and mark versions for all new APIs (#3526) * [DLMED] clarify old APIs Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * 3533 Update PyTorch docker to 21.12 (#3534) * [DLMED] update to 21.12 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add PyTorch 1.9 test Signed-off-by: Nic Ma <[email protected]> * 3531 Add args to subclass of CacheDataset (#3532) * [DLMED] add missing args Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update progress arg Signed-off-by: Nic Ma <[email protected]> * 3525 Fix invertible issue in OneOf compose (#3530) * [DLMED] fix oneof Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update index Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * Revert "[DLMED] update according to comments" This reverts commit c6c3a35. Signed-off-by: Nic Ma <[email protected]> * Revert "[DLMED] update index" This reverts commit 649a7c5. Signed-off-by: Nic Ma <[email protected]> * 3535 - drop python 36 support (#3536) * drop py36 support Signed-off-by: Wenqi Li <[email protected]> * drop 20.09 test because of python min version 3.6 Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * error->warning, revise copyright Signed-off-by: Wenqi Li <[email protected]> * 3541 has cupy check (#3544) * has cupy check Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * 3053 release *_dist.py tests memory to avoid OOM (#3537) * adds min. memory testing utils Signed-off-by: Wenqi Li <[email protected]> * include valueerror for robust outcome Signed-off-by: Wenqi Li <[email protected]> * ensure float Signed-off-by: Wenqi Li <[email protected]> * msg improvements Signed-off-by: Wenqi Li <[email protected]> * update threshold Signed-off-by: Wenqi Li <[email protected]> * remove ref Signed-off-by: Wenqi Li <[email protected]> * separate disttests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * 3539 Remove decollate warning (#3545) * [DLMED] remove warning Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance set_determinism (#3547) Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]> * Smooth Deform (#3551) * Adding smooth deform transform Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Docs update Signed-off-by: Eric Kerfoot <[email protected]> * Type fixing Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix for moveaxis Signed-off-by: Eric Kerfoot <[email protected]> * Fix for moveaxis Signed-off-by: Eric Kerfoot <[email protected]> * Adding example images, random field sized reduced to (10,10,10) Signed-off-by: Eric Kerfoot <[email protected]> * Changed backend Signed-off-by: Eric Kerfoot <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Tweak Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]> * 3552 - runtest.sh defaults to no build/install (#3555) * runtest.sh defaults to no build/install Signed-off-by: Wenqi Li <[email protected]> * following test case conventions for multiprocessing - adding `_dist` to multiprocessing test cases - decouple multiprocessing LMDB tests from `test_lmdbdataset` Signed-off-by: Wenqi Li <[email protected]> * exclude lmdbdataset tests in min_tests Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]> * Remove apply_same_field (#3556) Signed-off-by: Eric Kerfoot <[email protected]> * skipping pretraining network loading when downloading is unsuccessful (#3558) Signed-off-by: Wenqi Li <[email protected]> * [DLMED] fix mypy errors (#3562) Signed-off-by: Nic Ma <[email protected]> * 3559 Enhance `DatasetSummary` for several points (#3560) * [DLMED] update dataset summary Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance data type Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]> * add box util in monai/data * add box util in monai/data * [pre-commit.ci] pre-commit suggestions (#3568) updates: - [github.com/pre-commit/pre-commit-hooks: v4.0.1 → v4.1.0](pre-commit/pre-commit-hooks@v4.0.1...v4.1.0) - [github.com/asottile/pyupgrade: v2.29.0 → v2.31.0](asottile/pyupgrade@v2.29.0...v2.31.0) - [github.com/asottile/yesqa: v1.2.3 → v1.3.0](asottile/yesqa@v1.2.3...v1.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * 3565 - adds metadata when loading dicom series (#3566) * adds metadata when loading dicom series Signed-off-by: Wenqi Li <[email protected]> * fixes timed tests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * 3580 - create codeql-analysis.yml (#3579) * Create codeql-analysis.yml Signed-off-by: Wenqi Li <[email protected]> * build cpp Signed-off-by: Wenqi Li <[email protected]> * fixes Multiplication result converted to larger type Signed-off-by: Wenqi Li <[email protected]> * fixes url parsing Signed-off-by: Wenqi Li <[email protected]> * 498 Add logger_handler to LrScheduleHandler (#3570) * [DLMED] add log handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] test CI Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix logging Signed-off-by: Nic Ma <[email protected]> * [DLMED] temp test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix wrong unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix wrong test cases Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> Co-authored-by: Richard Brown <[email protected]> Co-authored-by: Ebrahim Ebrahim <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Description
This PR make some improvement in NVTX Range.
Status
Ready
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.